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The objective of the game is to clear the stage of cookies, which appear from the top and the right of the screen. To clear cookies, the player needs an entire row of the same cookies either horizontally or vertically. To move the cookies, the player has to press // on a cookie and press a direction on the directional pad. Depending on the direction the player presses, the row the cookie is on is then moved either vertically or horizontally. There are six types of cookies: heart cookies, sunflower cookies, green cookies, checkered cookies, ring shaped cookies, and Yoshi Cookies (shaped like Yoshi's head). The game consists of three modes: Action, VS, and Puzzle.

Action Mode is a game consisting of 10 rounds, with each round containing 10 stages. Before the game starts, the player can set the round which who wants to play in, the falling speed of the blocks and the music. After the player beats a certain stage, who can view a short, humorous cutscene with Mario. Rounds 11-99 are also unlockable, and within them the cookies are replaced by Mario enemies (except for the Yoshi Cookie).

VS Mode is a simple 2 player/1 player vs. COM game. The player starts off by picking one of four characters: Mario, Peach, Yoshi, or Bowser. The goal of the game is to keep a lit fuse higher or it runs out and all the player's pieces go away. To keep the fuse higher, the player have to consistently clear rows of 5 against the player's opponent. Getting 5 Yoshi cookie's in a row would often give the player a special, such as the players covering up the player's opponent's screen with question mark blocks or taking control of the opponent field.

The SNES version was developed and published by Bullet-Proof Software as they retained the rights for the SNES version and Nintendo licensed the characters and allowed them to use the "Yoshi's Cookie" Branding. Alexey Pajitnov, creator of Tetris, designed the puzzles.

Round 2: Mario chases after the rolling ball, only ends up rolling with the ball when grabbing on.

Round 3: Mario chases after the rolling ball, only to be humorously chased away by a larger bouncing ball (implied to be its parent)

Round 4: The ball bounces before hitting a wall, which then causes it to roll backwards into Mario (who was right behind it), knocking him over while the ball spins erratically.

Round 5: The ball spins erratically as Mario chases after it, only to end up eaten by Yoshi, to Mario's shock and Yoshi's amusement.

Round 6: Mario chases the ball down a slope, only to end up overtaking it in speed.

Round 7: The ball rolls then hits a wall and rolls back, with Mario proceeding to jump, only to end up squishing the ball.

Round 8: The ball falls down a ledge after rolling. Mario chases after it, only to find himself tripping due to unknowingly being on the ball, and the ball rolling away as Mario falls onto his back.

Round 9: The ball rolls to a cliffside as Mario chases after it, only for the ball to fall off the cliff, and ascend as an angel, with Mario looking sheepishly at the player.

Round 10: The ball is rolling and Mario and Yoshi, from opposite sides of the screen, proceed to grab it and then strike poses alongside the ball.

In the SNES version, the ball was revealed to be part of the Yoshi Cookie sign that fell off, and also has a slight animation of what occurs, and in the final one has Peach and Bowser joining the celebration during the credits.

In the NES and Game Boy versions, there was a cutscene at the title screen where Mario would walk onto a screen with a jar of cookies. He would then try to open it, to no avail. He then gets an idea and walks off the screen. Yoshi comes up soon after and eats the jar whole. Mario then reappears with a hammer and begins chasing Yoshi off the screen. Later, he returns back on screen holding the cookie jar, which was empty to begin with. This, however, bears no influence on the game itself. This intro (slightly expanded to show Yoshi and Mario re-congregating and then striking a pose before walking off) was made for the SNES prototype of the game, but was taken out for final release.

The SNES version of Yoshi's Cookie featured a slightly-updated version of Yoshi's appearance, in which he has a bigger head, longer and more human-like arms and shorter neck. This appearance would be later used in Super Mario All-Stars, Super Mario World 2: Yoshi's Island and later games. This game also marks the first time in-game that Yoshi's speech comprises of his name, a trait later used in Yoshi's Story and popularized by Super Smash Bros..